I am running WP 3.9.1. Fresh install. ACF and Gravity Forms are the only two plugins running.

Perhaps someone had this issue before...

On the edit menu screen I have a tab called "View All" where I can see all pages and children pages under them. That's where you would typically check each box and make your menu. However in some cases the children pages are showing up as parent pages. It makes no sense. I know that this does not affect where the pages go in the actual menu. But it's an issue nonetheless.

Screenshot:

Actual parent page and children pages:

Pages showing in the edit menu screen correctly (but missing 3):

Pages showing in the edit menu screen as parent pages instead of children

Any ideas? I checked each page again and in the edit page screen they do indeed show as child page.

This is just one example, it happens with other pages and child pages too.